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Visualising data§

You can visualise your DICOM images directly from XNAT with the OHIF Viewer.

To visualise all data for a subject§

  • Navigate to the subject report page:
  • From your project home, click the subject name under the Subjects tab at the bottom of the page
  • Or, from the top menu, click Browse > Data > Subjects and select the subject from the list
  • Or, use the XNAT search to find the subject
  • From the Actions menu choose View Subject to launch the OHIF Viewer

View Subject

To visualise data for a particular session§

  • Navigate to the session report page:
  • From your project home, click the subject name under the Subjects tab at the bottom of the page, and then select the appropriate session
  • Or, from the top menu, click Browse > Data > (session type) and select the session from the list
  • Or, use the XNAT search to find the session
  • From the Actions menu choose View Session to launch the OHIF Viewer

View Session

Using the OHIF Viewer§

OHIF Viewer

View a different scan§

The available scans in this project are shown on the left.

  • Visualise a scan by double-clicking or dragging into the main viewer
  • Use the Previous and Next buttons in the toolbar to switch the current scan.
  • Use the Scans | XNAT Nav buttons to switch between showing thumbnails of the scans and a tree view of the XNAT data

View a different subject§

  • Click the XNAT Nav button at the top-left to show a tree view of the XNAT data
  • Under This Project click + next to the project name to expand the list of subjects
  • Select the eye icon next to the subject you wish to view
  • You can also go straight to particular sessions by clicking + next to the subject name to show the list of sessions.

View a different project§

  • Click the XNAT Nav button at the top-left to show a tree view of the XNAT data
  • Under Other Projects click + next to the project name to expand the list of subjects
  • Select the eye icon next to the subject you wish to view
  • You can also go straight to particular sessions by clicking + next to the subject name to show the list of sessions.

View more than one scan§

  • Click the Layout button in the OHIF Viewer toolbar and choosing a panel layout.

Visualisation Layout

Return to XNAT§

  • Click the browser back button to return to XNAT

Image navigation§

Use the OHIF Viewer toolbar at the top to select visualisation tools. Some tools are shown by clicking the More button. Some tools have keyboard and mouse shortcuts.

  • Manual cine: Use the scroll wheel to move through the image slices
  • Zoom: Select the Zoom tool (or press Z) and drag the mouse
  • Pan: Select the Pan tool (or press P) and drag the mouse
  • Rotate image: Press the , and . keys (More > Left and More > Right tools)
  • Horizontal flip image: Press H or click More > Flip H
  • Vertical flip image: Press V or click More > Flip V
  • Animated cine: Select the Cine tool and use the movie controls to continually cine through the image slices
  • Synchronise: When viewing multiple scans, the Sync checkbox will attempt to synchronise the slice location for the checked scans
  • Smooth Uncheck Smooth to show the true image produced by the scanner. Check Smooth to artificially smooth (interpolate) the voxels to make it seem like a higher-resolution image. This gives images a more natural appearance, but may blur region boundaries and does not accurately reflect the underlying data. For these reasons, caution should be used when performing measurements with smoothing enabled.

Visualisation tools§

  • Window/Level: Select the Levels tool (or press L) and drag the mouse
  • Magnify: Press M or click More > Magnify and drag the mouse to temporarily magnify a region
  • Probe: Click More > Probe and drag the mouse over the image to show the coordinates and values of data at the current mouse position

Annotations§

  • You can add simple annotations such as text labels and length or angle measurements, but note these may not be preserved between sessions

Contours and segments§